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7. Example problemsΒΆ

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The LAMMPS distribution includes an examples sub-directory with + + +

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7. Example problems +

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The LAMMPS distribution includes an examples sub-directory with several sample problems. Each problem is in a sub-directory of its own. Most are 2d models so that they run quickly, requiring at most a couple of minutes to run on a desktop machine. Each problem has an @@ -146,252 +20,111 @@ input script (in.*) and produces a log file (log.*) and dump file coordinates as additional input. A few sample log file outputs on different machines and different numbers of processors are included in the directories to compare your answers to. E.g. a log file like -log.crack.foo.P means it ran on P processors of machine “foo”.

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For examples that use input data files, many of them were produced by -Pizza.py or setup tools described in the -Additional Tools section of the LAMMPS -documentation and provided with the LAMMPS distribution.

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If you uncomment the dump command in the input script, a +log.crack.foo.P means it ran on P processors of machine "foo". +

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For examples that use input data files, many of them were produced by +Pizza.py or setup tools described in the +Additional Tools section of the LAMMPS +documentation and provided with the LAMMPS distribution. +

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If you uncomment the dump command in the input script, a text dump file will be produced, which can be animated by various -visualization programs. It can -also be animated using the xmovie tool described in the Additional Tools section of the LAMMPS documentation.

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If you uncomment the dump image command in the input +visualization programs. It can +also be animated using the xmovie tool described in the Additional +Tools section of the LAMMPS documentation. +

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If you uncomment the dump image command in the input script, and assuming you have built LAMMPS with a JPG library, JPG snapshot images will be produced when the simulation runs. They can be quickly post-processed into a movie using commands described on the -dump image doc page.

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Animations of many of these examples can be viewed on the Movies -section of the LAMMPS WWW Site.

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These are the sample problems in the examples sub-directories:

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balancedynamic load balancing, 2d system
bodybody particles, 2d system
colloidbig colloid particles in a small particle solvent, 2d system
combmodels using the COMB potential
crackcrack propagation in a 2d solid
cudause of the USER-CUDA package for GPU acceleration
dipolepoint dipolar particles, 2d system
dreidingmethanol via Dreiding FF
eimNaCl using the EIM potential
ellipseellipsoidal particles in spherical solvent, 2d system
flowCouette and Poiseuille flow in a 2d channel
frictionfrictional contact of spherical asperities between 2d surfaces
gpuuse of the GPU package for GPU acceleration
hugoniostatHugoniostat shock dynamics
indentspherical indenter into a 2d solid
inteluse of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor
kimuse of potentials in Knowledge Base for Interatomic Models (KIM)
lineline segment particles in 2d rigid bodies
meamMEAM test for SiC and shear (same as shear examples)
meltrapid melt of 3d LJ system
micelleself-assembly of small lipid-like molecules into 2d bilayers
minenergy minimization of 2d LJ melt
msstMSST shock dynamics
nb3buse of nonbonded 3-body harmonic pair style
nebnudged elastic band (NEB) calculation for barrier finding
nemdnon-equilibrium MD of 2d sheared system
obstacleflow around two voids in a 2d channel
peptidedynamics of a small solvated peptide chain (5-mer)
periPeridynamic model of cylinder impacted by indenter
pourpouring of granular particles into a 3d box, then chute flow
prdparallel replica dynamics of vacancy diffusion in bulk Si
qequse of the QEQ pacakge for charge equilibration
reaxRDX and TATB models using the ReaxFF
rigidrigid bodies modeled as independent or coupled
shearsideways shear applied to 2d solid, with and without a void
snapNVE dynamics for BCC tantalum crystal using SNAP potential
srdstochastic rotation dynamics (SRD) particles as solvent
tadtemperature-accelerated dynamics of vacancy diffusion in bulk Si
tritriangular particles in rigid bodies
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Here is how you might run and visualize one of the sample problems:

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cd indent
+dump image doc page.
+

+
Animations of many of these examples can be viewed on the Movies
+section of the LAMMPS WWW Site.
+

+
These are the sample problems in the examples sub-directories:
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balance  dynamic load balancing, 2d system
body     body particles, 2d system
colloid  big colloid particles in a small particle solvent, 2d system
comb	  models using the COMB potential
crack	  crack propagation in a 2d solid
cuda     use of the USER-CUDA package for GPU acceleration
dipole   point dipolar particles, 2d system
dreiding methanol via Dreiding FF
eim      NaCl using the EIM potential
ellipse  ellipsoidal particles in spherical solvent, 2d system
flow	  Couette and Poiseuille flow in a 2d channel
friction frictional contact of spherical asperities between 2d surfaces
gpu      use of the GPU package for GPU acceleration
hugoniostat Hugoniostat shock dynamics
indent	  spherical indenter into a 2d solid
intel    use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor
kim      use of potentials in Knowledge Base for Interatomic Models (KIM)
line     line segment particles in 2d rigid bodies
meam	  MEAM test for SiC and shear (same as shear examples)
melt	  rapid melt of 3d LJ system
micelle  self-assembly of small lipid-like molecules into 2d bilayers
min	  energy minimization of 2d LJ melt
msst	  MSST shock dynamics
nb3b     use of nonbonded 3-body harmonic pair style
neb	  nudged elastic band (NEB) calculation for barrier finding
nemd	  non-equilibrium MD of 2d sheared system
obstacle flow around two voids in a 2d channel
peptide  dynamics of a small solvated peptide chain (5-mer)
peri	  Peridynamic model of cylinder impacted by indenter
pour     pouring of granular particles into a 3d box, then chute flow
prd      parallel replica dynamics of vacancy diffusion in bulk Si
qeq      use of the QEQ pacakge for charge equilibration
reax     RDX and TATB models using the ReaxFF
rigid    rigid bodies modeled as independent or coupled
shear    sideways shear applied to 2d solid, with and without a void
snap     NVE dynamics for BCC tantalum crystal using SNAP potential
srd      stochastic rotation dynamics (SRD) particles as solvent
tad      temperature-accelerated dynamics of vacancy diffusion in bulk Si
tri      triangular particles in rigid bodies 
+

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+
Here is how you might run and visualize one of the sample problems:
+

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cd indent
 cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
-lmp_linux -in in.indent            # run the problem
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Running the simulation produces the files dump.indent and -log.lammps. You can visualize the dump file as follows:

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../../tools/xmovie/xmovie -scale dump.indent
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If you uncomment the dump image line(s) in the input +lmp_linux -in in.indent # run the problem + +

Running the simulation produces the files dump.indent and +log.lammps. You can visualize the dump file as follows: +

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../../tools/xmovie/xmovie -scale dump.indent 
+
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If you uncomment the dump image line(s) in the input script a series of JPG images will be produced by the run. These can be viewed individually or turned into a movie or animated by tools like ImageMagick or QuickTime or various Windows-based tools. See the -dump image doc page for more details. E.g. this +dump image doc page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a -browser.

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% convert -loop 1 *.jpg foo.gif
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There is also a COUPLE directory with examples of how to use LAMMPS as +browser. +

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% convert -loop 1 *.jpg foo.gif 
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There is also a COUPLE directory with examples of how to use LAMMPS as a library, either by itself or in tandem with another code or library. -See the COUPLE/README file to get started.

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There is also an ELASTIC directory with an example script for -computing elastic constants, using a zero temperature Si example. See -the in.elastic file for more info.

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There is also a USER directory which contains subdirectories of +See the COUPLE/README file to get started. +

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There is also an ELASTIC directory with an example script for +computing elastic constants at zero temperature, using an Si example. See +the ELASTIC/in.elastic file for more info. +

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There is also an ELASTIC_T directory with an example script for +computing elastic constants at finite temperature, using an Si example. See +the ELASTIC_T/in.elastic file for more info. +

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There is also a USER directory which contains subdirectories of user-provided examples for user packages. See the README files in those directories for more info. See the -Section_start.html file for more info about user -packages.

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